I don't see how rigging is related to morph data. All lines from the original morph file should be preserved. Only the morph deltas are changed. If you want to keep your morph file, then open both files in a text editor, side-by-side. Copy the delta values from fixed morph file to your morph file.

Hi! It did wonders on my G2 morph, whose pupils were int eh wrong spot on the eyeballs, but left the eyes a bit too close together (fixable by your eye LR adjustment), but more importantly, unrigged (so the rotate morphs now just translate them). Do you know the solution?